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PubMed2003

Protein separation by nonsynchronous coil planet centrifuge with aqueous-aqueous polymer phase systems.

Counter-current chromatographic separation of proteins was performed using a rotary-seal-free nonsynchronous coil planet centrifuge (CPC) fabricated in our laboratory. This apparatus has a unique feature that allows a freely adjustable rotational rate of the coiled separation column at a given revolution speed. The separation was performed using a set of stable proteins including cytochrome c, myoglobin and lysozyme with two different types of aqueous-aqueous polymer phase systems, i.e., PEG (polyethylene glycol) 1000-dibasic potassium phosphate, and PEG 8000-dextran T500 in 5 mM potassium phosphate buffer. Using a set of multilayer coiled columns prepared from 0.8 mm I.D. PTFE tubing with different volumes (11, 24, 39 ml), the effect of the column capacity on the partition efficiency was investigated under a given set of experimental conditions. Among these experiments, the best separation of proteins was attained using the 39 ml capacity column with a 12.5% (w/w) PEG 1000-12.5% (w/w) dibasic potassium phosphate system at 10 rpm of coil rotation under 800 rpm. With lower phase mobile at 0.2 ml/min in the head-to-tail elution, the resolution between cytochrome c and myoglobin was 1.6 and that between myoglobin and lysozyme, 1.9. With upper phase mobile in the head-to-tail elution, the resolution between lysozyme and myoglobin peaks was 1.5. In these two separations, the stationary phase retention was 35.0 and 33.3%, respectively. Further studies were carried out using a pair of eccentric coil assemblies with 0.8 mm I.D. PTFE tubing at a total capacity of 20 ml. A comparable resolution was obtained using both lower and upper phases as a mobile phase in a head-to-tail elution. The results of our studies demonstrate that the nonsynchronous CPC is useful for protein separation with aqueous-aqueous polymer phase systems.

Centrifugation↗
PubMed2001

Catalysis of peptide formation by inorganic oxides: high efficiency of alumina under mild conditions on the Earth-like planets.

Amino acid condensation catalyzed by inorganic oxides is a widely recognized way for prebiotic peptide formation. Silica and alumina are widely distributed in the Earth-like planets' crust as minerals of different complexity, and thus are attractive model catalysts for the studies of abiotic peptide synthesis. Experiments performed in other laboratories have shown that this process can be efficient at > 80 degrees C, which is not easy to find on the planetary surface in combination with sufficient concentrations of amino acids and necessary catalysts. In the present work we tested catalytic activity of three forms of alumina (which proved to be an efficient catalyst for this process) in the intermolecular condensation of L-alanine. We expanded the temperature interval down to 55 degrees C and used the simplest permanent heating procedure, without employing fluctuating drying/wetting conditions. The most important finding is that even under the lowest temperature considered (i.e. 55 degrees C), short peptide formation can be detected already after 10-30 days of heating. This fact implies that the abiotic peptide formation might occur in a wide variety of planetary environments, without need for high temperatures, given the presence of amino acid building blocks and alumina-containing minerals.

Alanine↗
PubMed2001

The formation of nitriles in hydrocarbon-rich atmospheres of planets and their satellites: laboratory investigations by the crossed molecular beam technique.

Crossed molecular beam experiments of cyano radicals, CN(X(2)Sigma(+)), reacting with unsaturated hydrocarbons have been performed to investigate synthetic routes to nitriles formation in hydrocarbon-rich atmospheres of planets and their moons. We have verified that all cyano radical reactions with acetylene, ethylene, methylacetylene, allene, benzene, and dimethylacetylene proceed without entrance barrier, have exit barriers well below the energy of the reactant molecules, and are strongly exothermic. The identification of the CN versus H atom exchange channel makes these reactions compelling candidates to synthesize unsaturated nitriles in solar system environments. Some of these nitriles, hitherto unobserved in our solar system, now represent an ideal target to be detected in the future Cassini-Huygens mission to Titan.

Journal Article↗
PubMed1970

The Earth as a planet.

A comparison of the Earth with the Moon and other planets can help considerably in the solving of geophysical problems. Professor Cook deals with some of these problems in this article, which is a summary of the inaugural lecture he gave as professor of geophysics at Edinburgh on January 15.

Journal Article↗
PubMed2006

Iron meteorites as remnants of planetesimals formed in the terrestrial planet region.

Iron meteorites are core fragments from differentiated and subsequently disrupted planetesimals. The parent bodies are usually assumed to have formed in the main asteroid belt, which is the source of most meteorites. Observational evidence, however, does not indicate that differentiated bodies or their fragments were ever common there. This view is also difficult to reconcile with the fact that the parent bodies of iron meteorites were as small as 20 km in diameter and that they formed 1-2 Myr earlier than the parent bodies of the ordinary chondrites. Here we show that the iron-meteorite parent bodies most probably formed in the terrestrial planet region. Fast accretion times there allowed small planetesimals to melt early in Solar System history by the decay of short-lived radionuclides (such as 26Al, 60Fe). The protoplanets emerging from this population not only induced collisional evolution among the remaining planetesimals but also scattered some of the survivors into the main belt, where they stayed for billions of years before escaping via a combination of collisions, Yarkovsky thermal forces, and resonances. We predict that some asteroids are main-belt interlopers (such as (4) Vesta). A select few may even be remnants of the long-lost precursor material that formed the Earth.

Journal Article↗
PubMed1994

Characteristic zonal winds and long-lived vortices in the atmospheres of the outer planets.

The cameras on board the NASA Voyager spacecraft provided a survey of cloud systems within the atmospheres of the giant planets and allowed determination of zonal wind patterns, which constrain long-lived cloud systems. The basic atmospheric circulations are compared and long-lived cloud features are reviewed. The basic structure of the Great Red Spot is reviewed and the tendency of the spot to drift at -4 m s(-1) or -2 m s(-1) is presented.

Journal Article↗
PubMed1994

Rossby solitary vortices, on giant planets and in the laboratory.

This is a review of laboratory experiments with a layer of shallow water having a free surface and rotating together with a vessel of parabolic form. Such a (rather original) setup has allowed one to create Rossby solitary vortex for the first time. The latter is an anticyclonic Rossby vortex not subjected to dispersive spread owing to its compensation by the nonlinearity of KdV type. By its structural, collisional, and other properties, including clear-cut cyclonic-anticyclonic asymmetry, it may be considered as a physical prototype of the large-scale long-lived anticyclonic Rossby vortices like the Great Red Spot of Jupiter or the Great Dark Spot of Neptune (this remarkable vortex was discovered by the spacecraft Voyager-2 during its farewell to the Solar System) and other vortices dominating in the atmospheres of giant planets and created by the unstable zonal flows. It has been shown that the vortex under study is a long-lived entity provided it satisfies "antitwisting condition," i.e., it has rather large amplitude (at which it rotates more quickly than it propagates and thereby carries the trapped fluid). In this case, it is not subjected to the "twisting" deformation and may be ascribed by the generalized Charney-Obukhov equation for Rossby vortices on shallow water with a free surface. The results of creating the vortex under consideration by the different methods have been compared with the results obtained by other authors in the experiments on shear-flow generation of Rossby vortices.

Journal Article↗
PubMed2006

Laser-driven shock experiments on precompressed water: Implications for "icy" giant planets.

Laser-driven shock compression of samples precompressed to 1 GPa produces high-pressure-temperature conditions inducing two significant changes in the optical properties of water: the onset of opacity followed by enhanced reflectivity in the initially transparent water. The onset of reflectivity at infrared wavelengths can be interpreted as a semiconductor<-->electronic conductor transition in water, and is found at pressures above approximately 130 GPa for single-shocked samples precompressed to 1 GPa. Our results indicate that conductivity in the deep interior of "icy" giant planets is greater than realized previously because of an additional contribution from electrons.

Journal Article↗
PubMed1999

Effect of elution modes on protein separation by cross-axis coil planet centrifuge with two different types of coiled columns.

Effect of elution modes on protein separation was investigated using cross-axis coil planet centrifuge (cross-axis CPC) with two different types of coiled columns, i.e., eccentric coil and toroidal coil assemblies. Myoglobin and lysozyme were separated with an aqueous two-phase solvent system composed of 12.5% (w/w) polyethylene glycol 1000 and 12.5% (w/w) dibasic potassium phosphate. The substantial effect of elution modes was observed by the toroidal coil, while the negative result was given at the eccentric coil. Using the toroidal coil, higher peak resolution of proteins was attained at the tail to head elution mode. In the outward lower phase mobile elution mode, the satisfactory separation was obtained by both eccentric coil and toroidal coil assemblies. However, in the inward upper phase mobile elution mode, the toroidal coil produced a broad and asymmetric myoglobin peak. The analysis using polyacrylamide gel electrophoresis revealed that the toroidal coil partially separated the components originally present in the myoglobin sample. As the result, a modified equation was devised to express the peak resolution (Rs) using the lysozyme peak. The overall results indicated that the toroidal coil produced better partition efficiency than the eccentric coil under the optimized experimental condition including the direction of the Coriolis force acting on the mobile phase in the toroidal coil.

Centrifugation↗
PubMed2005

The Living Planet Index: using species population time series to track trends in biodiversity.

The Living Planet Index was developed to measure the changing state of the world's biodiversity over time. It uses time-series data to calculate average rates of change in a large number of populations of terrestrial, freshwater and marine vertebrate species. The dataset contains about 3000 population time series for over 1100 species. Two methods of calculating the index are outlined: the chain method and a method based on linear modelling of log-transformed data. The dataset is analysed to compare the relative representation of biogeographic realms, ecoregional biomes, threat status and taxonomic groups among species contributing to the index. The two methods show very similar results: terrestrial species declined on average by 25% from 1970 to 2000. Birds and mammals are over-represented in comparison with other vertebrate classes, and temperate species are over-represented compared with tropical species, but there is little difference in representation between threatened and non-threatened species. Some of the problems arising from over-representation are reduced by the way in which the index is calculated. It may be possible to reduce this further by post-stratification and weighting, but new information would first need to be collected for data-poor classes, realms and biomes.

Animals↗
PubMed2002

Universal spectrum of two-dimensional turbulence on a rotating sphere and some basic features of atmospheric circulation on giant planets.

The Kolmogorov-Batchelor-Kraichnan (KBK) theory of two-dimensional turbulence is generalized for turbulence on the surface of a rotating sphere. The energy spectrum develops considerable anisotropy; a steep -5 slope emerges in the zonal direction, while in all others the classical KBK scaling prevails. This flow regime in robust steady state is reproduced in simulations with linear drag. The conditions favorable for this regime may be common for giant planets' atmospheric circulations; the same steep spectra are found in their observed zonal velocity profiles and utilized to explain their basic characteristics.

Journal Article↗
PubMed2005

BioMOBY successfully integrates distributed heterogeneous bioinformatics Web Services. The PlaNet exemplar case.

The burden of non-interoperability between on-line genomic resources is increasingly the rate-limiting step in large-scale genomic analysis. BioMOBY is a biological Web Service interoperability initiative that began as a retreat of representatives from the model organism database community in September, 2001. Its long-term goal is to provide a simple, extensible platform through which the myriad of on-line biological databases and analytical tools can offer their information and analytical services in a fully automated and interoperable way. Of the two branches of the larger BioMOBY project, the Web Services branch (MOBY-S) has now been deployed over several dozen data sources worldwide, revealing some significant observations about the nature of the integrative biology problem; in particular, that Web Service interoperability in the domain of bioinformatics is, unexpectedly, largely a syntactic rather than a semantic problem. That is to say, interoperability between bioinformatics Web Services can be largely achieved simply by specifying the data structures being passed between the services (syntax) even without rich specification of what those data structures mean (semantics). Thus, one barrier of the integrative problem has been overcome with a surprisingly simple solution. Here, we present a non-technical overview of the critical components that give rise to the interoperable behaviors seen in MOBY-S and discuss an exemplar case, the PlaNet consortium, where MOBY-S has been deployed to integrate the on-line plant genome databases and analytical services provided by a European consortium of databases and data service providers.

Computational Biology↗
PubMed1977

Osmotic fragility changes in preserved blood: measurements by coil planet centrifuge and parpart methods.

The coil planet centrifuge (CPC) can be used to measure the osmotic fragility of erythrocytes. Fragility measured by this method alters when different salts are used. The CPC and Parpart methods were used to measure the changes during storage in red cell osmotic fragility in ACD or CPD blood with or without adenine. More marked changes were detected by the CPC method, especially in old cells. The changes of fragility of erythrocytes during storage seem to occur mainly in old cells. Adenine is effective in preventing such changes.

Adenine↗
PubMed1996

The Morphogenesis of Bands and Zonal Winds in the Atmospheres on the Giant Outer Planets

The atmospheres of Jupiter, Saturn, Uranus, and Neptune were modeled as shallow layers of turbulent fluid overlying a smooth, spherical interior. With only the observed values of radius, rotation rate, average wind velocity, and mean layer thickness as model parameters, bands and jets spontaneously emerged from random initial conditions. The number, width, and amplitude of the jets, as well as the dominance of anticyclonic vortices, are in good agreement with observations for all four planets.

Journal Article↗
PubMed1997

A pulsar, the heliosphere, and pioneer 10: probable mimicking of a planet of PSR B1257+12 by solar rotation

Doppler data generated with the Pioneer 10 spacecraft's radio carrier wave between 1987 and 1995 show a 25.3-day periodicity which is related to the solar rotation. The timing data of the pulsar PSR B1257+12 also show a periodicity of 25.34 days, which has been explained as a signature of the pulsar's barycentric motion in response to the existence of a small moon-like object. However, because PSR B1257+12 is located close to the ecliptic and because the timing variations are in the range of microseconds, it is likely that the pulsar signal is affected by the same mechanism acting on the Pioneer 10 Doppler data. Hence, the hypothesized inner planet around PSR B1257+12 is probably an artifact of the heliosphere.

Journal Article↗
PubMed1999

Superionic and metallic states of water and ammonia at giant planet conditions.

The phase diagrams of water and ammonia were determined by constant pressure ab initio molecular dynamic simulations at pressures (30 to 300 gigapascal) and temperatures (300 to 7000 kelvin) of relevance for the middle ice layers of the giant planets Neptune and Uranus. Along the planetary isentrope water and ammonia behave as fully dissociated ionic, electronically insulating fluid phases, which turn metallic at temperatures exceeding 7000 kelvin for water and 5500 kelvin for ammonia. At lower temperatures, the phase diagrams of water and ammonia exhibit a superionic solid phase between the solid and the ionic liquid. These simulations improve our understanding of the properties of the middle ice layers of Neptune and Uranus.

Ammonia↗
PubMed1999

Dissociation of CH4 at high pressures and temperatures: diamond formation in giant planet interiors?

Experiments using laser-heated diamond anvil cells show that methane (CH4) breaks down to form diamond at pressures between 10 and 50 gigapascals and temperatures of about 2000 to 3000 kelvin. Infrared absorption and Raman spectroscopy, along with x-ray diffraction, indicate the presence of polymeric hydrocarbons in addition to the diamond, which is in agreement with theoretical predictions. Dissociation of CH4 at high pressures and temperatures can influence the energy budgets of planets containing substantial amounts of CH4, water, and ammonia, such as Uranus and Neptune.

Diamond↗
PubMed1996

Purification of mast cells with an improved nonsynchronous flow-through coil planet centrifuge.

A method for cell purification was designed without using high-density media which may impair membrane receptors. Rat and mouse mast cells were separated with an improved nonsynchronous flow-through coil planet centrifuge. Peritoneal cells were suspended at a concentration of 2-3x10(7) cells/ml in conditioned RPMI 1640, supplemented with 50% heat-inactivated FCS and 0.32% sodium citrate. In each separation 3 ml of cell suspension were loaded into the coiled column and elutriated at 4 degrees C. Several conditions, including the centrifugal force, revolution/rotation ratio, density of separation media, flow speed, and designs of both coiled column and flow tubes, were examined and optimized for mast cell purification. Rat mast cells were separated at the purity of 99.2%, with an average yield of 40% under sterile conditions. Nearly 90% pure mouse mast cells were harvested, despite a very low population of mast cells available in murine peritoneal cells. Purified cells were morphologically intact and discharged granules by exocytosis as indicated by electron-microscopic observations. The average histamine release with antigenic specificity was 34 and 61%, in passive sensitization in vitro and in vivo, respectively. Mast cells sensitized with mouse monoclonal IgE antibody released histamine, similar to cells sensitized with homologous antibody. This newly devised method of cell separation will be useful to purify biologically intact mast cells.

Animals↗